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d1x6za1

ID: 1513364523 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 117 (112)
Sequences: 647 (532.3)
Seq/Len: 5.777
Nf(neff/√len): 50.3

HHblits Results: (2016_02)
Sequences per length for each position, BEFORE the coverage/gap filter was applied

Legend: Dots above the red line, indicates positions where there is > 5 sequences per length (if visible, green bar = 20 seq/len). Point of this graphic is to give you an idea if resubmitting a sub-portion of your sequence might help increase the overall Seq/Len (which after applying the coverage filter is at: 5.777).

Sequences per length for each position, AFTER the coverage/gap filter was applied
Legend: If visible, the positions blocked in grey are regions that have > 75% gaps and were automatically trimmed and excluded in the GREMLIN analysis.

Trim query Generate MSA using: Filter MSA GREMLIN
Start: End: E-value: Iterations: Coverage: Remove gaps: Prior:

GREMLIN Results:
Residue pairs sorted by coevolution strength:

Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] covarying residues with sequence seperation > 3. The i and j are positions as given in the input sequence.

ij Scaled score Prob
103_C116_C2.8581.00
10_A76_F2.6581.00
105_S112_I2.4261.00
11_L90_I2.1811.00
75_T89_I2.1591.00
23_E27_R2.1421.00
4_R23_E2.0771.00
56_L74_L2.0651.00
112_I117_S1.8581.00
6_E55_K1.7951.00
4_R117_S1.6791.00
93_T104_T1.6731.00
107_Q112_I1.5540.99
3_A111_F1.5340.99
15_N18_K1.5270.99
9_S13_S1.4970.99
12_A15_N1.4600.99
24_A30_S1.4340.98
24_A28_G1.4250.98
91_T104_T1.4060.98
73_T91_T1.3870.98
13_S76_F1.3690.98
2_F5_S1.3520.97
17_L49_V1.3510.97
73_T89_I1.3120.97
89_I106_D1.3090.97
22_E94_R1.2900.96
4_R70_A1.2520.95
13_S56_L1.2480.95
13_S74_L1.2200.95
22_E99_G1.2160.94
36_G40_A1.2150.94
9_S74_L1.2030.94
101_W116_C1.2020.94
113_P116_C1.1820.93
13_S53_A1.1540.92
89_I112_I1.1530.92
11_L92_L1.1260.91
70_A94_R1.1230.91
6_E16_P1.1140.90
9_S56_L1.1100.90
24_A29_W1.0800.88
10_A13_S1.0730.88
11_L74_L1.0700.88
73_T93_T1.0560.87
103_C113_P1.0530.87
9_S55_K1.0330.85
4_R59_I1.0300.85
114_K117_S1.0190.84
6_E79_G1.0190.84
17_L53_A1.0180.84
Legend: Only predictions with Scaled Score > 1 are listed. For all 3L/2 predictions, click on one of the links below.
Prob = P(contact | scaled_score, seq/len).
Scaled Score = (raw_score/average(raw_scores)).
NEW Features
HHsearch Results: (06Aug15)
GREMLIN results overlayed on top 10 PDB hits:
Legend: Blue filled circles are GREMLIN results (Scaled Score > 1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on 10 HHsearch results which uses the overall probability and per-position alignment confidence. Inter oligomeric contacts in the pdb are in shades of red.
PDB M Cov P(%) HHΔ  
1qveA20.923199.60.252Contact Map
1x6zA10.982999.60.259Contact Map
3jyzA10.897499.60.281Contact Map
3sojA20.769299.30.387Contact Map
1oqwA20.982999.30.389Contact Map
2hi2A10.906990.465Contact Map
3sokA20.9573990.468Contact Map
4noaA10.8376630.825Contact Map
2m3kA10.90633.30.853Contact Map
2m7gA10.29916.40.895Contact Map
M = number of chains, if homo-oligomer
Cov = coverage of hit
P(%) = probability

Sequence Conservation (Image Generated using WebLogo v3)
Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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